file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 37.00 39.00 40.50 40.45 42.00 43.00
## [1] 40
## [1] 37 38 38 38 38 39 39 39 39 39 39 39 39 40 40 40 40 40 40 40 41 41 41 41 41
## [26] 42 42 42 42 42 42 42 42 42 42 42 42 42 43 43
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}
table(is.na(a2s))##
## FALSE TRUE
## 1739 261
##
## FALSE TRUE <NA>
## 21 1718 261
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: LRRC6 DNAAF11
## 2: C11orf49 CSTPP1
## 3: LINC00476 ERCC6L2-AS1
## 4: HNRNPA1P48 HNRNPA1L3
## 5: ZRANB2-AS2 ZRANB2-DT
## 6: LINC00271 AHI1-DT
## 7: RFX3-AS1 RFX3-DT
## 8: LINC00884 ATP13A3-DT
## 9: FBXO30-DT EPM2A-DT
## 10: LINC00894 EOLA2-DT
## 11: COX10-AS1 COX10-DT
## 12: LINC01184 SLC12A2-DT
## 13: FAM198B-AS1 GASK1B-AS1
## 14: C5orf17 LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16: LINC01146 HISLA
## 17: BTBD11 ABTB3
## 18: H2BU1 H2BC26
## 19: SKIV2L SKIC2
## 20: FAM155A NALF1
## 21: CTB-41I6.2 PIK3R5-DT
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CFTR CFTR CFTR
## 2: ICA1 ICA1 ICA1
## 3: PDK4 PDK4 PDK4
## 4: CALCR CALCR CALCR
## 5: ABCB4 ABCB4 ABCB4
## t1
## 1
## 2000
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp"
## reactome go_bp
## 1692 7647
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CFTR CFTR CFTR
## 2: ICA1 ICA1 ICA1
## [1] 36517 9
## gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003 FALSE TSPAN6 NCBITaxon:9606
## 2: ENSG00000000005 FALSE TNMD NCBITaxon:9606
## feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1: gene 76 0.002350 99.8100
## 2: gene 1 0.000025 99.9975
## total_counts
## 1: 94
## 2: 1
## [1] 2000
##
## TRUE
## 2000
##
## FALSE TRUE
## 34517 2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1
table(gene_dat$selected)##
## 0 1
## 34517 2000
## $`0`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 94.48 99.58 93.53 99.97 100.00
##
## $`1`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.6475 65.5944 84.3650 76.3053 93.6756 97.9950
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data",
by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)## [1] 2000 12
## sym_in_data sym_limma gene_symbol gene_ids feature_is_filtered
## 1: AATK AATK AATK ENSG00000181409 FALSE
## 2: ABAT ABAT ABAT ENSG00000183044 FALSE
## feature_reference feature_biotype n_cells_by_counts mean_counts
## 1: NCBITaxon:9606 gene 3157 0.091525
## 2: NCBITaxon:9606 gene 9074 0.368950
## pct_dropout_by_counts total_counts selected
## 1: 92.1075 3661 1
## 2: 77.3150 14758 1
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol",
bias.data = 100 - gene_info$pct_dropout_by_counts)
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "PFN2" "ABCC1" "STMN2" "FBN2" "NFIX" "VCAN"
## [7] "ABCA7" "FAM107B" "PLEKHH3" "ANO8" "RAP1GAP" "ITPKC"
## [13] "NDFIP2" "DGKH" "HSF4" "HAVCR1" "PFKFB4" "CYTIP"
## [19] "HIF3A" "HIP1" "KIF1A" "RAMP1" "KDM6B" "MACROD1"
## [25] "DNAJB2" "MYO1G" "GUK1" "CAMK4" "FBXO27" "GMEB1"
## [31] "ANKZF1" "OTUD1" "ZBTB7A" "TRNAU1AP" "TNFAIP8L3" "ZBTB7C"
## [37] "SESTD1" "CD247" "SLC12A8" "LUCAT1"
## [1] 2
## [1] "SP140" "GAREM1" "AZIN2" "LINC00467"
## [5] "HESX1" "UCN" "PLD4" "DENND2B"
## [9] "SPTLC3" "CYSLTR1" "MCMDC2" "CATSPERE"
## [13] "CAPS2" "CLEC9A" "LINC01285" "AC003090.1"
## [17] "LINC01357" "TMEM72-AS1" "FTCDNL1" "RP11-162D16.2"
## [21] "RFX3-AS1" "LINC02642" "RPL34-DT" "RP11-195C7.1"
## [25] "COX10-AS1" "RNF217-AS1" "GMDS-DT" "RP11-745L13.2"
## [29] "CTC-575N7.1" "MIR3142HG" "RP11-630C16.2" "RP11-554D14.6"
## [33] "RP11-72M17.1" "RP11-187O7.3" "RP11-323I15.5" "MIR222HG"
## [37] "RP11-323P17.2" "EIF1B-AS1" "RP11-281A20.2" "RP11-323F24.5"
## [41] "RP11-111G13.1" "RP11-120L14.1"
## [1] 3
## [1] "SYNDIG1" "CPED1" "ARL5C" "SESN3"
## [5] "ENPP3" "C4orf19" "DEPTOR" "GHRL"
## [9] "ADAMTS15" "MIR31HG" "MICOS10" "MARCHF3"
## [13] "KBTBD12" "MAMDC2-AS1" "LINC00539" "HCG22"
## [17] "AC002539.1" "RP5-1198O20.4" "RP11-634B7.4" "LINC01141"
## [21] "AC073115.6" "KCNMB2-AS1" "LINC02008" "RP11-246A10.1"
## [25] "XACT" "LINC02057" "LINC01258" "AC008697.1"
## [29] "LINC02232" "MAILR" "RP11-946L16.1" "LINC02444"
## [33] "RP11-588H23.3" "RP11-399K21.11" "LINC02712" "CCDC28A-AS1"
## [37] "LINC00506" "RP11-437L7.2" "RP11-168F24.3" "RP11-685G11.1"
## [41] "RP1-236J16.3" "RP11-4F5.3"
## [1] 4
## [1] "DUOX1" "C11orf65" "ADGRG2" "ENO4"
## [5] "FSIP2" "AC002463.3" "ELMO1-AS1" "TMLHE-AS1"
## [9] "SLC8A1-AS1" "AC105461.1" "AC096558.1" "WEE2-AS1"
## [13] "AC092431.3" "FSIP2-AS1" "RNASEH2B-AS1" "RP11-353M9.1"
## [17] "RP11-528G1.2" "RP11-666F17.1" "RP11-123B3.2" "MYCBP2-AS1"
## [21] "DIAPH2-AS1" "CCDC200" "AC018890.6" "MEF2C-AS2"
## [25] "RP11-360F5.1" "CTD-2227I18.1" "RP11-268P4.5" "RP11-238K6.1"
## [29] "RP11-649G15.2" "RP11-463D19.1" "RP11-196H14.2" "RP11-513G19.1"
## [33] "RP11-493L12.3" "RP11-136F16.1" "LMO7-AS1" "RP11-621L6.2"
## [37] "RP11-793A3.2" "CTD-2282P23.2" "RP11-305E17.8" "DISC2"
## [41] "RP11-1146N6.3" "RP11-314E10.1" "RP3-467L1.4"
## [1] 5
## [1] "TRIM2" "PTPRB" "MEIS1" "BTD"
## [5] "FIGN" "ZNF804B" "RP11-640F22.1" "CNTN1"
## [9] "ADGRL1" "CELF4" "CDH20" "FLT1"
## [13] "ITGB8" "DNAH6" "MICAL2" "ZNF365"
## [17] "ADGRL3" "SPOCK1" "SCN3A" "CACNA2D1"
## [21] "PTPRN2" "SYN2" "FGF17" "SPTBN4"
## [25] "PDZRN4" "ZFPM2" "FUT9" "CDH4"
## [29] "GPC5" "TSHZ2" "PBX1" "SYN3"
## [33] "MIB2" "TOX" "RORB" "SOGA3"
## [37] "RP11-384F7.2" "MTRNR2L1"
## [1] 6
## [1] "CELSR3" "SYT7" "CSMD2" "PCSK2"
## [5] "ATP8A2" "RBMS3" "TENM2" "CNTN5"
## [9] "ZNF385D" "AK5" "NCAM2" "CFAP251"
## [13] "CLSTN2" "NRG2" "CAMK2N1" "ANKRD30BL"
## [17] "GABRB1" "PRICKLE2" "CSMD3" "LRFN5"
## [21] "GREM1" "SEMA3E" "HPSE2" "LRRC3B"
## [25] "KCTD16" "FLRT2" "PTPRT" "CR1L"
## [29] "ZNF521" "LINC00970" "LINC00632" "FAM155A"
## [33] "MIAT" "AC013463.2" "SHISA9" "AC002066.1"
## [37] "RP11-79E3.2" "CTC-535M15.2" "RP11-20D14.3" "IQCJ-SCHIP1"
## [41] "RP4-799O8.1" "RP5-1015P16.1" "RP11-398J12.1"
## [1] 7
## [1] "ZFP64" "PLAGL1"
## [3] "SPATA6" "PEBP4"
## [5] "ARMH4" "MTHFD2L"
## [7] "NMNAT3" "ARHGAP42"
## [9] "ATF7IP2" "TMC7"
## [11] "ACYP2" "ZDHHC14"
## [13] "C5orf64" "SPATA13_ENSG00000182957"
## [15] "KCNQ3" "SCFD2"
## [17] "PRKN" "MBD5"
## [19] "MIR99AHG" "HMGA1P4"
## [21] "MEF2C-AS1" "CTB-161M19.4"
## [23] "MRPS30-DT" "ARHGAP6"
## [25] "KCNQ2" "PILRA"
## [27] "BICRAL" "SLC26A7"
## [29] "NPAS3" "FUT10"
## [31] "ZHX2" "KCNQ5"
## [33] "GLDN" "NPIPB15"
## [35] "ZNF846" "ZDBF2"
## [37] "LNCAROD" "MYO16-AS1"
## [39] "LINC02646" "HCG17"
## [41] "RP11-114N19.3" "RP11-358F13.1"
## [1] 8
## [1] "TMSB10" "TPD52" "OXCT1" "SUSD1" "MAP2K6" "ALDOC" "CCDC18"
## [8] "MTHFS" "TBC1D32" "FOXO1" "CLIC2" "IER2" "C1QA" "ABAT"
## [15] "RPL39" "TWIST2" "FGR" "HGF" "CDK14" "CDK17" "DDX3Y"
## [22] "PGM1" "NAMPT" "TPI1" "SOD2" "USP9Y" "PAPOLG" "HSPH1"
## [29] "DOCK6" "ZNF331" "GNA12" "NEK7" "ETS2" "PTMS" "PCNT"
## [36] "AXL" "CLIC4" "GLRX" "FAM210A"
## [1] 9
## [1] "SNCAIP" "LRRC74A" "IL1A" "IL1B" "STON2" "MLIP" "MACROD2"
## [8] "ZNF707" "KCNIP1" "SKA2" "HECW1" "MATK" "PKD1" "CTNNA2"
## [15] "TRHDE" "RBFOX1" "PHLPP1" "EPHA4" "KDM5B" "EMILIN2" "FGF2"
## [22] "KCNH1" "SNTG1" "FMN2" "LRP1B" "DLGAP1" "KCND3" "DPP10"
## [29] "PCDH9" "EFNA5" "KCND2" "NELL2" "RALYL" "KCNIP4" "MAGI2"
## [36] "GRM7" "MICAL3"
## [1] 10
## [1] "ADAM28" "ST6GAL1" "APBB1IP" "TMEM156" "PLAC8" "KCNMB1"
## [7] "RASGEF1C" "KCNMA1" "TSPAN7" "AUTS2" "PRMT9" "NXN"
## [13] "ZNF608" "GPR34" "TLN2" "DLEU1" "SLC8A1" "SRGAP3"
## [19] "KIF9-AS1" "LINC01091" "MIR100HG" "PRANCR" "MRC1" "RNASET2"
## [25] "DOCK3" "PCSK5" "TMED8" "TIMP1" "RGCC" "LIFR"
## [31] "NR4A3" "TMEM115" "SLC2A5" "SPRY1" "RBFOX3" "DHRS13"
## [37] "ROBO1" "AIDA" "TSPAN4" "SNHG14"
## [1] 11
## [1] "OPHN1" "LRRC6" "RAB40B" "CFAP74"
## [5] "BEND6" "ADGRG5" "PLXDC1" "RNF180"
## [9] "CCDC171" "MT1E" "LINC00476" "PLCXD3"
## [13] "COL25A1" "AC007879.5" "ENTPD3-AS1" "TSBP1-AS1"
## [17] "RP11-445F6.2" "TEX41" "LMCD1-AS1" "RP13-188A5.1"
## [21] "LINC00271" "LINC02884" "RORA-AS1" "BDNF-AS"
## [25] "LINC02211" "MIR4300HG" "STX18-AS1" "RP11-130F10.1"
## [29] "RP11-692D12.1" "RP11-679C8.2" "LINC02055" "SMIM35"
## [33] "RP11-493L12.4" "LINC00639" "CTD-2336H13.2" "LINC01374"
## [37] "RP11-495L19.1" "RP11-622O11.6" "RP6-91H8.6" "RP4-545L17.11"
## [41] "RP11-321P16.3" "HTR1E"
## [1] 12
## [1] "SNX24" "ARHGEF18" "PDE4D" "XKR6"
## [5] "RP11-131L23.1" "SLC16A1-AS1" "JARID2" "MSR1"
## [9] "ARAP2" "PDE4A" "FAM50A" "CPSF1"
## [13] "PRKAG2" "TSHZ3" "SEM1" "FNBP1L"
## [17] "CAMKMT" "RSU1" "SLC2A13" "ACSL1"
## [21] "RPP38" "RASA2" "ST3GAL2" "ACOT11"
## [25] "MTSS1" "KLHL6" "SH3PXD2B" "PACS1"
## [29] "PDE4B" "OSBP2" "PARVB" "CTD-3088G3.8"
## [33] "COL27A1" "LINC00862" "AS3MT" "RP11-37N22.1"
## [37] "FAM229A" "AC067959.1" "RP11-13N12.1" "RP11-344F5.1"
## [41] "RP11-249L21.6"
## [1] 13
## [1] "EPB41L2" "EPB41L3" "TDRD3" "CALD1" "SMAD6" "STAMBPL1"
## [7] "ALDH7A1" "ZNRF1" "NSMAF" "AMPH" "IRAK3" "ARHGEF10"
## [13] "DOT1L" "PPARD" "RLF" "AKT3" "CTSD" "ELL2"
## [19] "RUNX2" "ARHGAP22" "IRAK2" "PHF21A" "GLUL" "FAM117B"
## [25] "PELI2" "USP53" "ARID5B" "RIT2" "PDE3B" "AGPAT5"
## [31] "EPB41" "RUNX1" "G6PD" "PPIP5K1" "TMEM51" "AFF1"
## [37] "PELI1" "RGL3"
## [1] 14
## [1] "PRDM11" "CD74" "P3H2" "NLRP1" "DAAM1" "ITPR2"
## [7] "ABCC4" "DOCK10" "LPAR6" "BCAS3" "MED12L" "CCDC102B"
## [13] "COPG2" "KIF26B" "ARHGAP25" "P2RY12" "NAALADL2" "CACNB4"
## [19] "DYNC2H1" "SLC1A3" "RFX3" "RFX2" "DOCK9" "LAPTM4B"
## [25] "RAPGEF1" "PTPRE" "SSH2" "SDK1" "FER" "MGAT5"
## [31] "FMNL2" "OXR1" "KIF5C" "BNC2" "KLC2" "LONRF3"
## [37] "OPCML" "GDI1" "NEAT1"
## [1] 15
## [1] "ETV1" "PRKCQ" "MGLL" "RPH3A" "PITPNM2" "RNF157"
## [7] "TAGAP" "ATF5" "GTF2IRD1" "ADAM22" "KCNAB2" "RAB27A"
## [13] "TNS1" "ZNF586" "PTPN4" "ARRDC2" "ADAP1" "NPDC1"
## [19] "DCUN1D4" "SASH1" "CCND3" "HPCAL1" "IQSEC2" "ZC4H2"
## [25] "GYPC" "RASGRP3" "MSI2" "MALT1" "C11orf80" "GOLIM4"
## [31] "LPL" "ALOX15B" "ZDHHC20" "CADM1" "IFNLR1" "ARL4C"
## [37] "CARD11" "UNC13B"
## [1] 16
## [1] "MCF2L2" "ANGPT2" "PROCR" "CST3"
## [5] "IL7" "NEK11" "MMP24" "SGCE"
## [9] "IER3" "PDE5A" "C1QC" "BTG2"
## [13] "PAQR3" "FILIP1L" "SLC35G2" "GRIK1"
## [17] "MIR4435-2HG" "OLR1" "H2BC4" "ENTPD1-AS1"
## [21] "RPL41" "RP4-568F9.6" "DENND6A-AS1" "RP11-452H21.1"
## [25] "RNF213-AS1" "ABHD15-AS1" "KCNQ1OT1" "MMP28"
## [29] "H2AC19" "LINC00624" "GS1-98E2.1" "TGFB2"
## [33] "RNMT" "COL5A1" "ALCAM" "PPM1E"
## [37] "H1-0" "CEBPD" "RP11-384C4.7"
## [1] 17
## [1] "DERA" "TYMP" "MAP3K8" "SLC2A9"
## [5] "FLVCR2" "TBC1D14" "EPSTI1" "BCL2A1"
## [9] "PTH2R" "PSTPIP2" "DISP1" "LY96"
## [13] "FAM227B" "PNMA3" "CHSY3" "RP11-154H12.3"
## [17] "SAMD4A" "LIMCH1" "GRK3" "MAN1A1"
## [21] "FRMD4B" "PADI2" "CDH26" "CHSY1"
## [25] "TLR2" "TIAM2" "SLC25A37" "CFDP1"
## [29] "CDCP1" "TNFRSF11B" "LRFN4" "SSTR2"
## [33] "TLR5" "CYRIA" "GK" "GCC2-AS1"
## [37] "STARD10" "ZNF407" "MIR181A1HG" "FMN1"
## [41] "RP11-368L12.1"
## [1] 18
## [1] "CASS4" "MPP2" "RP11-160E2.6" "LRRC7"
## [5] "ARHGAP10" "SLC26A3" "PCDH11Y" "CPE"
## [9] "MOB3B" "PDZD2" "SEMA6D" "CDH18"
## [13] "CLVS2" "CNKSR2" "CRIM1" "SORCS3"
## [17] "EDIL3" "ADGRV1" "NLGN1" "CTNND2"
## [21] "ADCY5" "CNTNAP2" "RESF1" "CADM2"
## [25] "RIMS2" "NRXN1" "CSMD1" "ANKS1B"
## [29] "PRKG1" "NRG3" "SLIT1" "POTEG"
## [33] "KAZN" "MEG3" "BASP1-AS1" "ROR1-AS1"
## [37] "LINC01320" "USP2-AS1" "CPEB2-DT" "LINC00558"
## [41] "RP11-81K2.1" "RP11-396B14.2"
## [1] 19
## [1] "OSBPL6" "RALGPS2" "SLC10A7" "F13A1" "GAS2L3" "MAGI1" "PTPN14"
## [8] "BACH1" "TIAM1" "FBXL13" "PLEKHA7" "SH3RF3" "NCKAP5" "PLEKHA5"
## [15] "RORA" "FNDC3B" "SMARCD3" "TBL1X" "TRPS1" "POU6F2" "MEGF9"
## [22] "DENND1A" "STARD13" "DENND4C" "CPNE8" "RGL1" "THRB" "FARP1"
## [29] "ASAP1" "LONRF1" "SRSF12" "AGAP1" "LDLRAD4" "FAM110B" "TANC2"
## [36] "PEAK1" "CHST15" "LIMK2" "SIPA1L1"
## [1] 20
## [1] "ICA1" "PER3" "GPATCH2" "GDAP1"
## [5] "WLS" "CCDC170" "ZRANB3" "CHN1"
## [9] "AHI1" "EFCAB11" "SPAG16" "TRPC1"
## [13] "IRAK1BP1" "MMS22L" "NRGN" "CACNA1D"
## [17] "SYCE2" "MAMDC2" "RIC3" "DTWD2"
## [21] "DENND5B" "LCLAT1" "SCAI" "HRH1"
## [25] "KCNMB2" "CARNMT1-AS1" "RANBP17" "ZNF10"
## [29] "RP11-413N10.3" "ATP9A" "GABRG2" "CACNA1B"
## [33] "CACNA1C" "FAT3" "PCDH7" "FRMD3"
## [37] "MSRA" "UNC5C" "RYR2"
## [1] 21
## [1] "DHRS9" "EPDR1" "MID1" "APBA1" "GCNT2"
## [6] "AKAP7" "NRN1" "DTD1" "METTL25" "MIS18BP1"
## [11] "LANCL2" "LYVE1" "SLC22A23" "IRF8" "AIG1"
## [16] "CD226" "TMEM169" "EMB" "S100Z" "GAP43"
## [21] "MBOAT1" "PROS1" "KIAA0825" "DNAH14" "CCDC7"
## [26] "C12orf75" "RASSF2" "IL27RA" "E2F3" "SLC16A10"
## [31] "KLHL24" "HELLS" "AFDN" "ZBTB46" "SLC41A2"
## [36] "SLC12A6" "PPP1R9A" "SERTAD2" "AC025171.1"
## [1] 22
## [1] "RIPOR2" "MCTP2" "GLT1D1" "TMEM151B"
## [5] "KIF5C-AS1" "MTRNR2L8" "TRG-AS1" "MAMLD1"
## [9] "GALNT16" "KATNAL1" "AK1" "SNX25"
## [13] "ADAM23" "ATP8A1" "PATJ" "PGGHG"
## [17] "PAM" "BTBD11" "PITPNC1" "FBXO32"
## [21] "ZFYVE28" "ARHGEF3" "RANBP3L" "AMER2"
## [25] "KLF13" "CXXC5" "TBC1D10C" "XKR9"
## [29] "AC093843.1" "SATB1-AS1" "RP11-47I22.3" "CYP1B1-AS1"
## [33] "SLC5A4-AS1" "RMST" "RP11-429A20.3" "FMNL1-DT"
## [37] "MTRNR2L12" "LINC00551" "CH507-528H12.1" "RP11-596C23.6"
## [41] "RENO1" "RP11-335E8.3"
## [1] 23
## [1] "MUSK" "EFR3B" "CECR2" "LIPG"
## [5] "NME3" "PLAT" "OGN" "ECM2"
## [9] "PLGRKT" "PODXL2" "SLC5A9" "GALNT12"
## [13] "PLAU" "FMO5" "ITM2C" "AIM2"
## [17] "GPR85" "TMEM52B" "BEAN1" "GLYATL1"
## [21] "ARSJ" "LTC4S" "RP11-281P23.2" "RP11-517O13.1"
## [25] "TSIX" "FSTL4" "SERPINE1" "GALNT18"
## [29] "SLC6A8" "LYPD5" "ARSK" "GPRC5C"
## [33] "MAMDC4" "DGAT1" "SH3BGRL2" "TBKBP1"
## [37] "AF064858.6" "ARHGEF25" "AGBL1"
## [1] 24
## [1] "SIGLEC1" "BEX1" "ADGRA3" "PAPSS2"
## [5] "PVT1" "LINC00923" "DISC1FP1" "ST3GAL1"
## [9] "TENM1" "STAB1" "HIVEP2" "HDHD5"
## [13] "MAP3K20" "LILRB5" "MXI1" "GTDC1"
## [17] "HS3ST2" "CEMIP2" "GPNMB" "NIBAN2"
## [21] "RASGEF1B" "ST18" "JAML" "PLPP3"
## [25] "ATOH8" "MCTP1" "TMTC2" "TPRG1"
## [29] "DPYD" "IARS1" "ERO1A" "DIRC3"
## [33] "TRHDE-AS1" "RP11-657O9.1" "RP11-696N14.1" "SELENOP"
## [37] "LINC02698" "CLEC5A" "LINC01138" "CH507-513H4.1"
## [41] "RP11-475M20.2"
## [1] 25
## [1] "SLC26A4" "PRTFDC1"
## [3] "PEX7" "ZSCAN5A"
## [5] "CDYL2" "SLC9A7"
## [7] "MYO9A" "ZFY"
## [9] "WNT2B" "DRAM1"
## [11] "PXDNL" "LRRC4C"
## [13] "CLEC1A" "ME3"
## [15] "AMN1" "NEK10"
## [17] "GPHN" "SLC35E3"
## [19] "SLC48A1" "FADS3"
## [21] "AC023469.1" "ARL17B"
## [23] "SGO1-AS1" "LINC01762"
## [25] "RP11-147G16.1" "RP11-154D17.1"
## [27] "RP11-305L7.3" "IFITM10"
## [29] "RP11-17A1.3" "SBF2-AS1"
## [31] "RP1-179N16.6" "LINC01609"
## [33] "RP11-351A11.1" "RP11-707P17.1"
## [35] "CTB-41I6.2" "RMRP_ENSG00000269900"
## [37] "SCARNA2_ENSG00000270066" "LL22NC03-2H8.5"
## [39] "AC003099.2" "C2orf27A"
## [1] 26
## [1] "PLPP1" "ADGRD1" "PLEK" "CYREN"
## [5] "CENPK" "PCBD2" "ERMN" "ARHGAP20"
## [9] "SLC49A4" "HERC6" "UBE2Q2" "WDPCP"
## [13] "ABCA5" "TMEM144" "NLGN4Y" "FGGY"
## [17] "B3GNT5" "TTTY14" "PCED1B" "MS4A4E"
## [21] "LINC02649" "RP11-202G18.1" "ZRANB2-AS2" "RP11-557H15.4"
## [25] "RP11-142A5.1" "LINC00894" "LINC01376" "ARHGAP8"
## [29] "GPRC5D-AS1" "RP11-381K20.2" "LINC01572" "H2BC7"
## [33] "RP11-419I17.1" "RP1-111C20.3" "RP11-19D22.1" "RP11-574F11.4"
## [37] "RP11-221G19.1" "SESN1" "STN1" "TMEM65"
## [41] "MFSD4B" "ZC3H6"
## [1] 27
## [1] "CARMIL1" "SSPN" "PIGC" "AGBL3"
## [5] "FOLR2" "CYTL1" "GLIPR1L1" "FLJ40194"
## [9] "DLEU7" "EYS" "FAM177B" "HNRNPA1P48"
## [13] "EDNRB-AS1" "LINC01375" "RP11-526K17.2" "RP11-142M10.2"
## [17] "SRGAP2-AS1" "COA6-AS1" "ARHGAP15-AS1" "IPO9-AS1"
## [21] "AC007682.1" "RAP2C-AS1" "UFL1-AS1" "ITGA9-AS1"
## [25] "FBXO30-DT" "LINC00996" "RP11-712B9.2" "RP11-796E2.4"
## [29] "LINC02742" "CTD-2537O9.1" "RP11-370I10.2" "RHOXF1-AS1"
## [33] "RP11-516C1.1" "ZNF528-AS1" "MIR223HG" "RP11-74J13.8"
## [37] "RP1-80B9.4" "RP11-237N2.1" "RP11-264E23.4" "RP11-7F3.1"
## [41] "AC009166.9" "RP11-56I23.2"
## [1] 28
## [1] "LILRB2" "HTR2B" "OVCH1-AS1" "GRAMD4"
## [5] "PPP1R15A" "GADD45B" "RNF24" "GYS1"
## [9] "IL4I1" "APBB3" "GBE1" "TREM1"
## [13] "CHI3L1" "GDF11" "PLXNC1" "RGS16"
## [17] "MYO10" "PLIN2" "HTR7" "TAMALIN"
## [21] "IER5" "NFIL3" "DDIT4" "PPP1R3B"
## [25] "BNIP3" "RBM44" "ADGRB1" "VMO1"
## [29] "ZNF395" "NHEJ1" "EFCAB2" "LILRB3"
## [33] "LIMD1-AS1" "ZSCAN31" "AF064858.8" "RP11-661A12.5"
## [37] "HIF1A-AS3" "MYOCOS" "CTD-2285E13.1"
## [1] 29
## [1] "SCMH1" "IPCEF1" "POLA1" "ARSB" "RCAN3"
## [6] "C3" "FOXP2" "RFC3" "GSTCD" "FRMD6"
## [11] "FRMD4A" "ANO10" "SFMBT1" "SOCS6" "LRRC8C"
## [16] "ATAD5" "CA8" "SLC9A9" "ZFP36L1" "SFMBT2"
## [21] "XIST" "SCIN" "CLEC16A" "WWC3" "ARHGAP15"
## [26] "CLNK" "FOXP1" "HPCAL4" "RASSF8" "ELK1"
## [31] "FAM13A" "CSGALNACT1" "MERTK" "JAZF1" "ADK"
## [36] "CRADD" "RNF150" "SAMD12" "MAML2" "PLCG2"
## [1] 30
## [1] "ZNF532" "MBNL3" "PIGL" "CD69"
## [5] "MTERF1" "TMEM241" "RALGPS1" "ADAMTS17"
## [9] "TMEM44" "AOPEP" "RAB28" "SMIM14"
## [13] "SLC9B1" "PGBD5" "CDIN1" "B3GLCT"
## [17] "PRDX6-AS1" "TMSB4X" "LIPE-AS1" "ALOX12-AS1"
## [21] "ZNF433-AS1" "RP11-535M15.1" "CTA-292E10.6" "LINC01278"
## [25] "LINC01184" "RP11-319G6.1" "RP11-37B2.1" "LIX1-AS1"
## [29] "LINC02328" "CEROX1" "LINC02666" "CH17-55D9.1"
## [33] "RP4-681L3.3" "OGFRL1" "ADCY3" "CCDC107"
## [37] "ABCG1" "MARCHF8" "KCNE1" "LINC00910"
## [41] "PIK3IP1-DT"
## [1] 31
## [1] "NEXMIF" "TRPM3"
## [3] "NIPAL2" "PDE10A"
## [5] "GNLY" "UNC80"
## [7] "IGSF11" "ADAMTS19"
## [9] "BANK1" "ADAMTS3"
## [11] "RFLNA" "RTN4RL1"
## [13] "COL5A2" "DOK6"
## [15] "LINC01277" "AC011288.2"
## [17] "RP3-525N10.2" "ALG1L9P_ENSG00000248671"
## [19] "RP11-673E1.1" "FAM66D"
## [21] "RP4-809F18.1" "PSMD7-DT"
## [23] "COPG2IT1" "LINC02885"
## [25] "RP11-320L2.1" "NALCN"
## [27] "FGF14" "KCNT1"
## [29] "CHD5" "OLFM1"
## [31] "CBLN2" "STXBP5L"
## [33] "PALM2AKAP2" "NEGR1"
## [35] "LSAMP" "CACNA1E"
## [37] "RP11-191L9.4" "CTC-340A15.2"
## [39] "RP11-259O2.1" "LINC01414"
## [41] "U91319.1" "RP11-436D23.1"
## [1] 32
## [1] "IFT43" "CGNL1" "EPHB2" "C11orf49"
## [5] "GASK1B" "RAB39A" "RNLS" "ERC2"
## [9] "CENPP" "ATP6AP1L" "FIRRE" "LINC01356"
## [13] "AC097721.2" "LINC01684" "C5orf17" "ATP6V0D1-DT"
## [17] "RP11-692P14.1" "LCP2" "ZFAT" "PAG1"
## [21] "PRAM1" "KIAA0513" "PPFIA2" "CCDC40"
## [25] "NR6A1" "DIXDC1" "SH3RF1" "CFAP161"
## [29] "ZNF143" "LPCAT4" "CCDC73" "SYCP2"
## [33] "LINC02397" "C17orf67" "RP5-864K19.4" "KLF3-AS1"
## [37] "AC092835.2" "RP11-111A21.1" "RP11-154H23.4" "RP11-404C6.6"
## [1] 33
## [1] "CALCR" "ACER3"
## [3] "CEACAM1" "HAMP"
## [5] "ADGRG6" "PARD3B"
## [7] "LDAH" "RAB38"
## [9] "PUDP" "NPL"
## [11] "CH25H" "NKD1"
## [13] "SAMSN1" "MAP3K7CL"
## [15] "TNFRSF13C" "PUS10"
## [17] "DNAJC24" "WDR25"
## [19] "SDHAF3" "LIN52"
## [21] "LINC00630" "LINC01515"
## [23] "CCDC26" "CDKN2B-AS1"
## [25] "LINC02432" "LINC01094"
## [27] "LINC01605_ENSG00000253161" "C8orf37-AS1"
## [29] "RP11-486A14.2" "LINC01146"
## [31] "LINC00907" "RP11-736I24.5"
## [33] "RP11-38B6.1" "RP13-52K8.2"
## [35] "TGFBI" "SEC14L1"
## [37] "PARP8" "IL15"
## [39] "APLF" "H2AC6"
## [41] "CTD-2643I7.5"
## [1] 34
## [1] "ATP5F1E" "ENOSF1" "XAF1" "IFI44L"
## [5] "ABCA8" "FHAD1" "PID1" "MOBP"
## [9] "ODF3B" "MX2" "HDAC4-AS1" "PCDH9-AS2"
## [13] "AC073115.7" "RP11-115J16.1" "LINC02073" "H2BC8"
## [17] "H2AC8" "SLC2A3" "PDE8A" "RGS1"
## [21] "DARS1" "SRGN" "BTG1" "HILPDA"
## [25] "CCNG2" "TNFAIP8" "ARHGAP18" "TMEM140"
## [29] "FRRS1" "ALDH1A1" "JAKMIP2" "ADSS1"
## [33] "ANKRD37" "H2BU1" "UBXN2B" "AC093818.1"
## [37] "DARS1-AS1" "MIR155HG" "SAP30-DT" "RP11-134L10.2"
## [1] 35
## [1] "PDK4" "HHAT" "TXNDC16" "ZNF821" "MS4A4A" "TENT5A"
## [7] "STX11" "BRIP1" "TNFRSF21" "NUBPL" "B2M" "PBX3"
## [13] "FTH1" "PTPRM" "RTTN" "GCLC" "GCLM" "PRKCH"
## [19] "HACE1" "CEP170B" "ANKRD12" "INTS6" "UBE2R2" "NCOA7"
## [25] "SOX5" "NHSL1" "CPM" "GFOD1" "RASSF3" "CDC42SE2"
## [31] "STARD9" "CLASP2" "SLMAP" "STXBP5" "ABCA1" "CHD2"
## [37] "GPRIN3" "RALGAPA2" "ZNF277" "DENND1B"
## [1] 36
## [1] "PKD2L2" "PCSK1N" "CRYM" "ANGPTL1"
## [5] "CALY" "BEX3" "RAB37" "SPDYE2"
## [9] "GOLGA8B" "SMCR5" "RP5-1132H15.1" "LANCL1-AS1"
## [13] "RMDN2-AS1" "KDM4A-AS1" "LRIG2-DT" "MEIKIN"
## [17] "RP11-544A12.8" "RP11-120A1.1" "RP11-506H20.1" "RP11-624C23.1"
## [21] "RP11-867G2.8" "RP11-571M6.7" "RP11-317G6.1" "RP11-66H6.3"
## [25] "LINC00621" "RP11-121C2.3" "RP11-275G7.2" "RP11-21M24.6"
## [29] "RP11-65F13.4" "RP11-617F9.2" "RASGRP2" "COL5A3"
## [33] "IGSF9B" "ARFGEF3" "SNED1" "FSTL5"
## [37] "STXBP6" "SRRM3" "H1-10" "FAM153CP"
## [41] "LINC01322" "RP11-322M13.1"
## [1] 37
## [1] "NEURL2" "ACKR4" "SHOC1" "H2AC20"
## [5] "H2BC18" "INSYN2B" "ANKUB1" "DOCK4-AS1"
## [9] "ARHGAP26-AS1" "AC017101.10" "AC037445.1" "RP11-575L7.8"
## [13] "CPB2-AS1" "RP11-775D22.3" "STARD4-AS1" "ANK2-AS1"
## [17] "CTD-2015H6.3" "AC006160.5" "RHOQ-AS1" "LINC02196"
## [21] "AP000487.6" "RP11-1H15.2" "RP11-638I2.8" "LINC02316"
## [25] "USP3-AS1" "RP11-815J21.4" "RP11-16B9.1" "RP11-106M3.3"
## [29] "RP11-16C1.3" "RP11-703M24.5" "CEACAM16-AS1" "TCF4-AS1"
## [33] "RP11-58G13.1" "RP11-126O1.4" "RP1-256G22.2" "RP11-386I14.4"
## [37] "RP11-793H13.14" "RP11-622I12.1" "RP11-314L11.1" "RP11-1H15.4"
## [41] "RP11-6G22.1" "RP11-555K12.4"
## [1] 38
## [1] "IGF1" "RPL3" "RPL18A" "RPL19"
## [5] "RPL34" "RPL24" "IFIT3" "IFIT2"
## [9] "FGF13" "RPLP1" "RPS24" "PRDM5"
## [13] "RPS2" "RPS11" "RPL11" "RPS27A"
## [17] "RPL32" "FAU" "ATG10" "RPL26"
## [21] "ELAVL4" "NFIA" "RPL38" "RPLP2"
## [25] "TSPYL2" "IFIT1" "RPS23" "SPATS2L"
## [29] "CPNE4" "RPL12" "RPL23A" "AIF1"
## [33] "RP11-511B23.2" "SPOCK2" "SLC1A2" "ZMAT4"
## [37] "ADARB1" "SKIV2L"
## [1] 39
## [1] "ABCB4" "NAV3" "TTC7A" "FAM149A"
## [5] "PLCL1" "GARNL3" "GIPC2" "GPAT3"
## [9] "GASK1A" "ITGA9" "DPYS" "TENM4"
## [13] "TMEM163" "SETBP1" "LIPC" "NAV2"
## [17] "CX3CR1" "ZMAT3" "TCERG1L" "RP1-30E17.2"
## [21] "AC105760.2" "MIR646HG" "HDAC2-AS2" "LINC00884"
## [25] "RP11-120D5.1" "PTCHD4" "LINC00968" "LINC02762"
## [29] "ZFPM2-AS1" "LINC01301" "RP11-10H3.1" "RP11-541P9.3"
## [33] "RP11-370I10.6" "MEI4" "CTTNBP2" "CUX2"
## [37] "DPYSL3" "WDR45B" "NCMAP" "EME2"
## [41] "LINC01435" "RP11-452F19.4"
## [1] 40
## [1] "ATP8B1" "OMD" "IRAG1-AS1" "SCOC-AS1"
## [5] "MTCP1" "RP11-321C24.1" "AC023590.1" "ZNF451-AS1"
## [9] "RP11-165F24.3" "ALG13-AS1" "RP1-225E12.2" "AC083884.8"
## [13] "RP1-117O3.2" "KCNMA1-AS1" "BCL2L1-AS1" "RP11-544A12.4"
## [17] "LINC01877" "RP5-1101C3.1" "ZBTB20-AS5" "LINC00960"
## [21] "FAM198B-AS1" "RP11-39E3.3" "CTD-3239E11.2" "RP11-434H14.1"
## [25] "RP1-71H24.1" "RP11-713N11.4" "CTD-2647E9.3" "PRKCA-AS1"
## [29] "RP11-737O24.2" "RP11-53B2.3" "CTD-3149D2.4" "RP4-769N13.7"
## [33] "RP11-354K4.2" "RP11-458A7.1" "RP11-261A24.1" "RP1-18C9.3"
## [37] "RP11-13J12.3" "RP11-685G9.5" "RP11-341N18.1" "RP11-399K19.1"
## [41] "CTD-2021K4.2" "CCDC71L"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_12"
## [1] "SNX24" "ARHGEF18" "PDE4D" "XKR6"
## [5] "RP11-131L23.1" "SLC16A1-AS1" "JARID2" "MSR1"
## [9] "ARAP2" "PDE4A" "FAM50A" "CPSF1"
## [13] "PRKAG2" "TSHZ3" "SEM1" "FNBP1L"
## [17] "CAMKMT" "RSU1" "SLC2A13" "ACSL1"
## [21] "RPP38" "RASA2" "ST3GAL2" "ACOT11"
## [25] "MTSS1" "KLHL6" "SH3PXD2B" "PACS1"
## [29] "PDE4B" "OSBP2" "PARVB" "CTD-3088G3.8"
## [33] "COL27A1" "LINC00862" "AS3MT" "RP11-37N22.1"
## [37] "FAM229A" "AC067959.1" "RP11-13N12.1" "RP11-344F5.1"
## [41] "RP11-249L21.6"
## $reactome
## category over_represented_pvalue under_represented_pvalue numDEInCat
## 203 darpp 32 events 4.013069e-05 1 3
## numInCat FDR
## 203 3 0.04743448
##
## [1] "set_14"
## [1] "PRDM11" "CD74" "P3H2" "NLRP1" "DAAM1" "ITPR2"
## [7] "ABCC4" "DOCK10" "LPAR6" "BCAS3" "MED12L" "CCDC102B"
## [13] "COPG2" "KIF26B" "ARHGAP25" "P2RY12" "NAALADL2" "CACNB4"
## [19] "DYNC2H1" "SLC1A3" "RFX3" "RFX2" "DOCK9" "LAPTM4B"
## [25] "RAPGEF1" "PTPRE" "SSH2" "SDK1" "FER" "MGAT5"
## [31] "FMNL2" "OXR1" "KIF5C" "BNC2" "KLC2" "LONRF3"
## [37] "OPCML" "GDI1" "NEAT1"
## $reactome
## category over_represented_pvalue
## 177 copi dependent golgi to er retrograde traffic 1.165260e-05
## 404 golgi to er retrograde transport 3.623322e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 177 0.9999999 3 6 0.01377338
## 404 0.9999997 3 7 0.02141383
##
## $go_bp
## category over_represented_pvalue
## 1515 microtubule based movement 6.518369e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 1515 0.9999997 6 34 0.0307667
##
## [1] "set_19"
## [1] "OSBPL6" "RALGPS2" "SLC10A7" "F13A1" "GAS2L3" "MAGI1" "PTPN14"
## [8] "BACH1" "TIAM1" "FBXL13" "PLEKHA7" "SH3RF3" "NCKAP5" "PLEKHA5"
## [15] "RORA" "FNDC3B" "SMARCD3" "TBL1X" "TRPS1" "POU6F2" "MEGF9"
## [22] "DENND1A" "STARD13" "DENND4C" "CPNE8" "RGL1" "THRB" "FARP1"
## [29] "ASAP1" "LONRF1" "SRSF12" "AGAP1" "LDLRAD4" "FAM110B" "TANC2"
## [36] "PEAK1" "CHST15" "LIMK2" "SIPA1L1"
## $reactome
## category over_represented_pvalue
## 427 heme signaling 4.611284e-06
## 899 rora activates gene expression 1.053191e-05
## 568 metabolism of steroids 5.977165e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 427 1.0000000 4 5 0.005450538
## 899 1.0000000 3 3 0.006224357
## 568 0.9999994 3 6 0.023550029
##
## [1] "set_29"
## [1] "SCMH1" "IPCEF1" "POLA1" "ARSB" "RCAN3"
## [6] "C3" "FOXP2" "RFC3" "GSTCD" "FRMD6"
## [11] "FRMD4A" "ANO10" "SFMBT1" "SOCS6" "LRRC8C"
## [16] "ATAD5" "CA8" "SLC9A9" "ZFP36L1" "SFMBT2"
## [21] "XIST" "SCIN" "CLEC16A" "WWC3" "ARHGAP15"
## [26] "CLNK" "FOXP1" "HPCAL4" "RASSF8" "ELK1"
## [31] "FAM13A" "CSGALNACT1" "MERTK" "JAZF1" "ADK"
## [36] "CRADD" "RNF150" "SAMD12" "MAML2" "PLCG2"
## $reactome
## category
## 738 polymerase switching
## 251 dna strand elongation
## 521 lagging strand synthesis
## 739 polymerase switching on the c strand of the telomere
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 738 6.050154e-05 1.0000000 2 2
## 251 1.574333e-04 0.9999996 2 3
## 521 1.574333e-04 0.9999996 2 3
## 739 1.596824e-04 0.9999996 2 3
## FDR
## 738 0.04718616
## 251 0.04718616
## 521 0.04718616
## 739 0.04718616
##
## [1] "set_35"
## [1] "PDK4" "HHAT" "TXNDC16" "ZNF821" "MS4A4A" "TENT5A"
## [7] "STX11" "BRIP1" "TNFRSF21" "NUBPL" "B2M" "PBX3"
## [13] "FTH1" "PTPRM" "RTTN" "GCLC" "GCLM" "PRKCH"
## [19] "HACE1" "CEP170B" "ANKRD12" "INTS6" "UBE2R2" "NCOA7"
## [25] "SOX5" "NHSL1" "CPM" "GFOD1" "RASSF3" "CDC42SE2"
## [31] "STARD9" "CLASP2" "SLMAP" "STXBP5" "ABCA1" "CHD2"
## [37] "GPRIN3" "RALGAPA2" "ZNF277" "DENND1B"
## $reactome
## category over_represented_pvalue
## 391 glutathione conjugation 9.802069e-05
## 392 glutathione synthesis and recycling 9.802069e-05
## 555 metabolic disorders of biological oxidation enzymes 9.802069e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 391 1 2 2 0.03862015
## 392 1 2 2 0.03862015
## 555 1 2 2 0.03862015
##
## [1] "set_38"
## [1] "IGF1" "RPL3" "RPL18A" "RPL19"
## [5] "RPL34" "RPL24" "IFIT3" "IFIT2"
## [9] "FGF13" "RPLP1" "RPS24" "PRDM5"
## [13] "RPS2" "RPS11" "RPL11" "RPS27A"
## [17] "RPL32" "FAU" "ATG10" "RPL26"
## [21] "ELAVL4" "NFIA" "RPL38" "RPLP2"
## [25] "TSPYL2" "IFIT1" "RPS23" "SPATS2L"
## [29] "CPNE4" "RPL12" "RPL23A" "AIF1"
## [33] "RP11-511B23.2" "SPOCK2" "SLC1A2" "ZMAT4"
## [37] "ADARB1" "SKIV2L"
## $reactome
## category over_represented_pvalue
## 138 cellular response to starvation 0
## 301 eukaryotic translation elongation 0
## 302 eukaryotic translation initiation 0
## 452 influenza infection 0
## 557 metabolism of amino acids and derivatives 0
## 640 nonsense mediated decay nmd 0
## 801 regulation of expression of slits and robos 0
## 850 response of eif2ak4 gcn2 to amino acid deficiency 0
## 901 rrna processing 0
## 927 selenoamino acid metabolism 0
## under_represented_pvalue numDEInCat numInCat FDR
## 138 1 19 26 0
## 301 1 19 23 0
## 302 1 19 23 0
## 452 1 19 27 0
## 557 1 19 41 0
## 640 1 19 23 0
## 801 1 19 27 0
## 850 1 19 25 0
## 901 1 19 25 0
## 927 1 19 26 0
##
## $go_bp
## category over_represented_pvalue
## 630 cytoplasmic translation 0.000000e+00
## 4283 ribosome biogenesis 2.297898e-10
## 4279 ribosomal large subunit biogenesis 1.496023e-08
## 4278 ribosomal large subunit assembly 5.804644e-07
## 4281 ribosomal small subunit biogenesis 2.788900e-06
## 4282 ribosome assembly 2.823109e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 630 1 19 23 0.000000e+00
## 4283 1 8 13 5.423040e-07
## 4279 1 5 5 2.353743e-05
## 4278 1 4 4 6.849480e-04
## 4281 1 4 5 2.220846e-03
## 4282 1 4 5 2.220846e-03
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8955058 478.3 16112782 860.6 NA 16112782 860.6
## Vcells 16667131 127.2 31295163 238.8 65536 31295163 238.8
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.10
## [4] fgsea_1.24.0 biomaRt_2.54.1 limma_3.54.2
## [7] tidyr_1.3.0 ggpubr_0.6.0 ggplot2_3.4.2
## [10] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 GenomeInfoDb_1.34.9
## [9] tools_4.2.3 backports_1.4.1
## [11] bslib_0.4.2 utf8_1.2.3
## [13] R6_2.5.1 mgcv_1.8-42
## [15] DBI_1.1.3 BiocGenerics_0.44.0
## [17] colorspace_2.1-0 withr_2.5.0
## [19] tidyselect_1.2.0 prettyunits_1.1.1
## [21] bit_4.0.5 curl_5.0.1
## [23] compiler_4.2.3 cli_3.6.1
## [25] Biobase_2.58.0 xml2_1.3.4
## [27] DelayedArray_0.24.0 rtracklayer_1.58.0
## [29] sass_0.4.5 scales_1.2.1
## [31] rappdirs_0.3.3 Rsamtools_2.14.0
## [33] stringr_1.5.0 digest_0.6.31
## [35] rmarkdown_2.21 XVector_0.38.0
## [37] pkgconfig_2.0.3 htmltools_0.5.5
## [39] MatrixGenerics_1.10.0 dbplyr_2.3.2
## [41] fastmap_1.1.1 rlang_1.1.0
## [43] rstudioapi_0.14 RSQLite_2.3.1
## [45] BiocIO_1.8.0 jquerylib_0.1.4
## [47] generics_0.1.3 jsonlite_1.8.4
## [49] BiocParallel_1.32.6 dplyr_1.1.2
## [51] car_3.1-2 RCurl_1.98-1.12
## [53] magrittr_2.0.3 GO.db_3.16.0
## [55] GenomeInfoDbData_1.2.9 Matrix_1.6-4
## [57] Rcpp_1.0.10 munsell_0.5.0
## [59] S4Vectors_0.36.2 fansi_1.0.4
## [61] abind_1.4-5 lifecycle_1.0.3
## [63] stringi_1.7.12 yaml_2.3.7
## [65] carData_3.0-5 SummarizedExperiment_1.28.0
## [67] zlibbioc_1.44.0 org.Hs.eg.db_3.16.0
## [69] BiocFileCache_2.6.1 grid_4.2.3
## [71] blob_1.2.4 parallel_4.2.3
## [73] crayon_1.5.2 lattice_0.20-45
## [75] splines_4.2.3 Biostrings_2.66.0
## [77] cowplot_1.1.1 GenomicFeatures_1.50.4
## [79] hms_1.1.3 KEGGREST_1.38.0
## [81] knitr_1.44 pillar_1.9.0
## [83] GenomicRanges_1.50.2 rjson_0.2.21
## [85] ggsignif_0.6.4 codetools_0.2-19
## [87] stats4_4.2.3 fastmatch_1.1-3
## [89] XML_3.99-0.14 glue_1.6.2
## [91] evaluate_0.20 png_0.1-8
## [93] vctrs_0.6.2 gtable_0.3.3
## [95] purrr_1.0.1 cachem_1.0.7
## [97] xfun_0.39 broom_1.0.4
## [99] restfulr_0.0.15 rstatix_0.7.2
## [101] tibble_3.2.1 GenomicAlignments_1.34.1
## [103] AnnotationDbi_1.60.2 memoise_2.0.1
## [105] IRanges_2.32.0